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fix output glob (#1552)

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Matthias De Smet 2022-04-22 13:04:41 +02:00 committed by GitHub
parent b1749445d7
commit c17d1a7a7b
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2 changed files with 3 additions and 3 deletions
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4
modules/elprep/filter/main.nf
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@ -23,7 +23,7 @@ process ELPREP_FILTER {
output: output:
tuple val(meta), path("**.{bam,sam}") ,emit: bam tuple val(meta), path("output/**.{bam,sam}") ,emit: bam
tuple val(meta), path("*.metrics.txt") ,optional: true, emit: metrics tuple val(meta), path("*.metrics.txt") ,optional: true, emit: metrics
tuple val(meta), path("*.recall") ,optional: true, emit: recall tuple val(meta), path("*.recall") ,optional: true, emit: recall
tuple val(meta), path("*.vcf.gz") ,optional: true, emit: gvcf tuple val(meta), path("*.vcf.gz") ,optional: true, emit: gvcf
@ -65,7 +65,7 @@ process ELPREP_FILTER {
def assembly_regions_cmd = get_assembly_regions ? " --assembly-regions ${prefix}.assembly_regions.igv": "" def assembly_regions_cmd = get_assembly_regions ? " --assembly-regions ${prefix}.assembly_regions.igv": ""
""" """
elprep filter ${bam} ${prefix}.${suffix} \\ elprep filter ${bam} output/${prefix}.${suffix} \\
${reference_sequences_cmd} \\ ${reference_sequences_cmd} \\
${filter_regions_cmd} \\ ${filter_regions_cmd} \\
${markdup_cmd} \\ ${markdup_cmd} \\

2
tests/modules/elprep/filter/test.yml
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@ -6,7 +6,7 @@
files: files:
- path: output/elprep/test.activity_profile.igv - path: output/elprep/test.activity_profile.igv
- path: output/elprep/test.assembly_regions.igv - path: output/elprep/test.assembly_regions.igv
- path: output/elprep/test.bam - path: output/elprep/output/test.bam
- path: output/elprep/test.g.vcf.gz - path: output/elprep/test.g.vcf.gz
- path: output/elprep/test.metrics.txt - path: output/elprep/test.metrics.txt
- path: output/elprep/test.recall - path: output/elprep/test.recall